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<CENTER><A HREF = "http://pizza.sandia.gov">Pizza.py WWW Site</A> - <A HREF = "Manual.html">Pizza.py Documentation</A> - <A HREF = "Section_tools.html">Pizza.py Tools</A> 
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<H3>vmd tool 
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<P><B>Purpose:</B>
</P>
<P>Control VMD from python.
</P>
<P><B>Description:</B>
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<P>The vmd tool is a simple wrapper on the <A HREF = "http://www.ks.uiuc.edu/Research/vmd">VMD visualization
package</A>, a popular tool for visualizing snapshots from molecular
dynamics simulations.
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<P>The vmd constructor invokes VMD in its own window.  Data can be passed
to it for visualization via the new(), data(), replace(), and append()
methods.  The other methods permit more specialized interactions with
VMD through its command syntax.
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<P><B>Usage:</B>
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<PRE>v = vmd()		       start up VMD
v.stop()		       shut down VMD instance
v.clear()		       delete all visualizations 
</PRE>
<PRE>v.rep(style)		       set default representation style. One of
			       (Lines|VDW|Licorice|DynamicBonds|Points|CPK) 
v.new(file[,type])   	       load new file (default file type 'lammpstrj')
v.data(file[,atomstyle])       load new data file (default atom style 'full')
v.replace(file[,type])	       replace current frames with new file
v.append(file[,type]) 	       append file to current frame(s)
v.set(snap,x,y,z,(True|False)) set coordinates from a pizza.py snapshot to new or current frame 
</PRE>
<PRE>v.frame(frame)		       set current frame
v.flush()		       flush pending input to VMD and update GUI
v.read(file)		       read Tcl script file (e.g. saved state) 
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<PRE>v.enter()		       enter interactive shell
v.debug([True|False])	       display generated VMD script commands? 
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<P><B>Related tools:</B>
</P>
<P><A HREF = "gl.html">gl</A>
</P>
<P><B>Prerequisites:</B>
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<P>Python pexpect package.
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